From 95f3da1126ee3f7db6c10101f6f66437e1400dbb Mon Sep 17 00:00:00 2001
From: carneiro <carneiro@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 10 Jun 2011 20:14:30 +0000
Subject: [PATCH] limiting the number of reads in memory for the
 SamValidateFile.jar

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5976 348d0f76-0448-11de-a6fe-93d51630548a
---
 scala/qscript/core/DataProcessingPipeline.scala | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scala/qscript/core/DataProcessingPipeline.scala b/scala/qscript/core/DataProcessingPipeline.scala
index 90372fb62..a6fda9d24 100755
--- a/scala/qscript/core/DataProcessingPipeline.scala
+++ b/scala/qscript/core/DataProcessingPipeline.scala
@@ -418,7 +418,7 @@ class DataProcessingPipeline extends QScript {
     @Output(doc="validation log") var validate = outLog
     override def inputBams = List(inBam)
     override def outputBam = outLog
-    override def commandLine = super.commandLine + " VALIDATE_INDEX=true MODE=SUMMARY REFERENCE_SEQUENCE=" + qscript.reference
+    override def commandLine = super.commandLine + " VALIDATE_INDEX=true MAX_RECORDS_IN_RAM=100000 MODE=SUMMARY REFERENCE_SEQUENCE=" + qscript.reference
     sortOrder = null
     this.jarFile = qscript.validateSamJar
     this.isIntermediate = false